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tcd004 (134130) writes "Few sciences are more romantic than taxonomy. Imagine Darwin, perched over a nest of newly-discovered birds in the Galapagos, sketching away with a charcoal in his immortal journals. Yet Taxonomy is a dying science. DNA barcoding, which can identify species from tiny fragments of organic material, and other genetic sciences are pulling students away from the classical studies of anatomy and species classifications. As the biodiversity crisis wipes undiscovered species off the planet, so to go the scientists who count them."

DNA isn't pulling people away from taxonomy so much as replacing it with a vastly superior system. Classical taxonomy is kind of like classical mechanics. It's fine for most purposes, but it's not "complete" and its answers range from slightly inaccurate to flat out wrong depending on the question.

We no longer have to arbitrarily decide "ok, this is a new species because it's different in this way" we can now look at DNA and see exactly how it differs, what it's closest to, who its ancestors are, when it split, and so on. Names are inaccurate representations for humans to use. With DNA, the term "species" itself becomes somewhat irrelevant because we now know the system of species and genetics is much more fluid than that.

Exactly right, but it's worth warning there are still a lot of issues with the subject, not least the fact that in changing the way taxonomy is done there is confusion about what taxonomy is meant to actually achieve.

On one hand you have people who want easy names for things, so they can refer to them in conversation, or write books. Hey look at this "Blah blah" plant and so on.

On the other you have the needs of science - the need to be able to explicitly define a cut off point to say this is a different species, a different genus, a different family or whatever.

Historically taxonomy has had problems without DNA analysis because it's been based pretty much entirely on how a plant looks, it's features. If Plant A is a small fat round green cactus with 1 inch spines and small purple flowers and Plant B has the same then they must be the same species, or at least the same genus. This sounds well and good, but the advent of DNA analysis sometimes shows that plant A and plant B are in fact extremely genetically distinct and aren't closely related at all. So why did they look the same? Convergent evolution - if the two plant populations were 200 miles apart directly north-south to each other and the species that pollinates them likes small purple flowers then they've simply evolved the same traits through natural selection because of that pollinator. Meanwhile another plant 100 miles to the East of plant A may be a large tall thin cactus with a blue powdery coat and large white flowers but actually ends up being more genetically similar to the point it's in the same genus as plant A - it looks completely different because although it shares ancestry it's on the path of a completely different pollinator that likes tall blue plants with massive white flowers. The net result is that plants that are genetically close are not identified as such based on visual inspection, whilst those that aren't close are lumped together when they shouldn't be using classical taxonomy. This is why the AC above says classic taxonomy is sometimes outright wrong. Looks don't tell us anything like the sort of picture we need to know - without being able to track the growth and evolution of species through time we simply do not know the ancestry, so until the arrival of DNA taxonomy was a fundamentally flawed science.

So it seems like DNA solves everything right? Wrong. The problem we have now is that it's still arbitrary as to where you decide the cut off, how different does a subject have to be to be a distinct species from another subject? If their DNA varies by 0.00000000001% we can probably agree they're closely related enough to be the same species, but what about a 0.1% difference? what about a 1% difference? When we figure that out we then have to decide the boundaries for genus, for families, and also in the other direction for subspecies and so forth. Right now there is no fixed figure so it's still arbitrary - one taxonomist is separating species based on a 0.1% difference, and another is doing it on a 0.15% difference. This means we still have nonsense arguments about what genus a species belongs in or whatever - nonsense because it's completely down to personal opinion, and that's subjective.

The problem is that if we do do something objective and say right, well, the cut off points are 0.1% for species, 1% for genus and so on we end up with situations where subjects are lumped together in a manner that are inconvenient for the trade world, and for gardeners "Oh I've always called it that, I'm not changing the name, they need the same growing conditions so I'm going to treat them like they always used to be named" - sometimes the objective system can result in surprising classifications that are inconvenient for non-scientific users and so they refuse to adopt them.

Which takes us back to the original question - what is the point in taxonomy? From there we have to ask things like who does it exist to serve? What are it's goals? Does science even need it? would scientists be better off moving to a w

To add to your points, the big problem with taxonomy is that it treats two closely related species as if there is a definitely dividing line between them so that every animal can be categorized.

In reality, categorizing closely related species should probably be treated more like making a Venn diagram. Sometimes two species will have a definite dividing line between them, sometimes there's some overlap (especially when you get into tracing the evolution of species).

Yep, exactly. We can't really say that speciation is analog, it's not, it's defined by a finite albeit with an unimaginably large number of DNA variations, but it's absolutely a broad spectrum rather than a clear discrete set of possibilities which is what taxonomy tries to apply.

Because of that it's also hard to determine a dividing line from the perspective that what might look like a reasonable dividing line for say, very simple plant life, might not be a reasonable dividing line for a complex mammal. So

That's true. People scoff at the older taxonomic groupings from before we had molecular evidence, but actually I'm often surprised at how similar new phylogenies are to huge chunks of the old taxonomies. What's more, at least with plants, one molecular study can produce quite a different looking evolutionary tree to another depending on what genes they used to compute them.

Which begs the quesiton... what's the ground truth? Data from classical taxonomy is actually extremely valuable. It can help inform mole

"That's true. People scoff at the older taxonomic groupings from before we had molecular evidence, but actually I'm often surprised at how similar new phylogenies are to huge chunks of the old taxonomies."

I'm sure that depends on the families and genus in question, because certainly for Cactaceae it's made a complete mockery of previous taxonomic definitions.

"(i.e. cites the taxnomic publication which specifies what they mean when they use the name)."

Amusingly I tried to help a botanist do exactly this, we couldn't because although we found a snippet on Google Books of the original reference for the name, we couldn't see the whole thing because it unfortunately fell under the specific set of restrictions that meant it wont be out of copyright until about 2021, despite the fact it went out of print in about 1926 and the author died in about 1953 or something. I thought this was a fantastic example of how absurdly long copyright laws prevent scientific progress.

Even that works on a spectrum though depending how far removed they are from each other. Obviously one breed of sheep can breed with the same breed of sheep easily, success rate is ever so slightly lower between different breeds of sheep, but sometimes you can go as far as breeding a goat with a sheep to get a geep (yes really!) though the chance is far lower.

It's more obvious in the plant world when you can more easily attempt to cross pollinate different many different species and see the results often mu

So it seems like DNA solves everything right? Wrong. The problem we have now is that it's still arbitrary as to where you decide the cut off, how different does a subject have to be to be a distinct species from another subject? If their DNA varies by 0.00000000001% we can probably agree they're closely related enough to be the same species, but what about a 0.1% difference? what about a 1% difference?

Or it may be exactly which DNA differs. Possibly also exactly where that DNA is. It would theoretically b

DNA isn't pulling people away from taxonomy so much as replacing it with a vastly superior system. Classical taxonomy is kind of like classical mechanics. It's fine for most purposes, but it's not "complete" and its answers range from slightly inaccurate to flat out wrong depending on the question.

We no longer have to arbitrarily decide "ok, this is a new species because it's different in this way" we can now look at DNA and see exactly how it differs, what it's closest to, who its ancestors are, when it split, and so on. Names are inaccurate representations for humans to use. With DNA, the term "species" itself becomes somewhat irrelevant because we now know the system of species and genetics is much more fluid than that.

I'm not so sure Taxonomy has been replaced, it's just gotten a whole new and better tool and I suppose you could say the geneticists have kind of taken it over. In anthropology ancient DNA extraction where classification into species was done using skeletal morphology, DNA is likely to cause a whole lot of re-arrangement of the taxonomic classifications. When Svante Pääbo found Neanderthal DNA in modern humans he effectively threw the scientific equivalent of a hand grenade into the comfortably organized world of anthropology. His discovery shattered a widely accepted axiom and left a whole lot of people red-faced who'd been postulating that modern human admixture with archaic hominids was unlikely to the point of it being impossible. Technically modern non-African people belong to both the species H. Sapiens and H. Neanderthalensis, so the borderlines between species have all of a sudden become much more fuzzy thanks to geneticists. A really interesting recent development is that geneticists have found traces of extinct hominid populations that are only known from DNA analysis of living humans, not from discovered remains. Africans for example are now know to have interbred with archaic hominid populations but no physical specimens, i.e. skeletal samples of these archaic populations have ever been found so in that sense Africans aren't pure H. Sapients either. So we now have palaeontologist/archaeologists out in the field searching for physical remains of these 'shadow' or 'ghost' populations which has turned the normal practice in their field completely on it's head where you first found the bones and then took them to the lab for (DNA and other) analysis. As we get better at extracting DNA from ancient remains it will completely upend a lot of what we thought we knew about the mechanism of evolution.

I don't know whether or not this is actually happening (if not, no problem); but the one possible negative would be if genetic techniques are pulling people away from field work in favor of sequencing stuff and then number-crunching on it.

While the classical taxonomists are mere stamp collectors by the standards of phylogenetics, the field did have the virtue of getting people to slog to the godforsaken malarial back end of nowhere to look for new and exotic stuff. Given the rate at which the godforsaken

I'm good friends with a modern day plant hunter who is also a professional botanist, and who also has a number of discoveries and subsequent names under his belt.

I've never really asked him how the profession is doing in general, but from what I know of him the bottleneck as much as anything seems to be the amount of time it takes to describe a new species. Maybe he specifically is just very detailed in what he does, but for each discovery of a plant he has to provide illustration of it in growth, in flower

If taxonomy is really a dying science, you'd have a hard time telling from the number of species being described. According to reptile-database.org, there were 3149 snake species in 2008, as of Feb 2014, there are 3458. That's 309 species, 51 species a year, roughly a 10% increase in six years- which is stunning when you consider that we have been naming species since the 1700s. There were 5079 lizards in 2008, and 5914 in 2014. That's 835 species,139 a year, and a 16% increase. This is just the reptiles; y

What is your point precisely? Taxonomy is about determining the number of species and the boundaries between them- whether that means identifying a new population, or subdividing one group into two distinct species. Either one is taxonomy in action, the fact that we are seeing a dramatic increase in the number of species means that taxonomy is an active field, not a dying one.

The point is that it takes an awful lot less people to do automatic reclassification through DNA analysis than it does to go out into the field and actually find new species.

So whilst the number of distinctly defined species may be increase, the number of people actually working in the field could be decreasing, and if the determination of distinction is just the result of a taxonomist that favours splitting over lumping and is just arbitrary anyway then it's quite possible that an increasing number of clas

As a professional systematist**, this is the kind of claptrap I have to deal with on a daily basis. I use both types of data (morphological and DNA) and people should understand that molecular biology does not replace morphological taxonomy, but it provides another useful source of data. What is used for DNA data these days are a tiny part (especially DNA barcodes) of the functional organism, and the phenotype comes about in ways we do not completely understand yet. Because of the attitude shown in this po

Schools teach about voyages of discovery. They forget to teach that it wasn't about discovery it was about imperialism

If one defines "imperialism" as subjugation of peoples, then the case of the Galapagos Island was not imperialism: while Native Americans may have visited the island in prehistory, there was no human population on the islands when Europeans visited, and the endemic nature was the sole attraction. For Dawin, it really was a voyage of discovery.

Unfortunately for you, imperialism is defined as "a policy of extending a country's power and influence through diplomacy or military force."

Now, to the layman this poses no cuntradiction against your erudite proposal. However, the educated Marxist will not allow to pass your blatant speciesism. While the "Native" "Americans" are clearly irrelevant Redskin savages, as even the most niggardly capitalists/Hayek-ists will admit, we cannot allow to pass unchallenged and critically unexamined the acts of this Da

All that serves to tell us is that imperialism came with benefits, and that without imperialism there would not have been the resources to ship scientists around the world to do some of the most important and ground breaking science in history.

Or is that too inconvenient to your pre-conceived notion that nothing good ever came out of imperialism? If so then you're suffering from a case of "What did the Romans ever do for us?".

Sometimes good can come from bad, without World War II we'd never have had quite s

If DNA sequencing means taxonomy is now straightforward, then it's good students are switching to other fields. The goal of science is to solve problems, not to ossify. In this case, while taxonomy may cease to be a significant research field, morphology (understanding the structure and evolution of plants and animals) is surely going to continue. The people doing it will simply not be called "taxonomists" anymore.

During the 80s and 90s there were different projects trying to determine the cosmological parameters (mass density, curvature, cosmological constant, Hubble constant, etc). Then WMAP [wikipedia.org] was launched in 2001, and by 2006 (release of 3-year data) the previous techniques were obsolete. Do you think many students in 2001 started working on the old techniques? Should they have? But we haven't lost interest in the cosmological parameters.

So, if this is true, can someone tell me why the hell we need "bankers" anymore?

The purpose of banks has never been "to keep track" of your money. The purpose of banks has always been to keep your money safe. At least, that is supposed to be the reason for their existence.

The idea of fractional-reserve banking, i.e. making loans and so on with that hoard of money, came later. But that still doesn't mean their purpose is to track your money. If you weren't doing that yourself anyway -- at ANY time in history -- you were likely to lose that money.

The problem is that DNA sequencing doesn't mean taxonomy is now straightforward, on the contrary it's created an identity crisis as to what the subject is even meant to achieve anymore. See my post here for a broader description of what I mean:

It used to be simple when DNA analysis wasn't available and the actual ancestry was hidden by time, back then you could name stuff based on things that were convenient for science at the time, and people who just wanted to know what to call things alike. Nowadays there's a stark divide between the two, the science has uncovered that it's not that simple, and in doing so has uncovered the fact that taxonomy as a science would not be useful for one of the things it has been historically most useful for, which wouldn't be a problem in itself if it weren't for the fact that for it to become a true science, it needs to cast of the shackles of the general public, and the business world alike, something which as I'm sure you can imagine is quite difficult given the vested interests involved and even within the profession of taxonomy itself. Getting people to change their ways isn't easy.

Right, so you think choosing subjective opinion over objective fact is scientific?

For something to be a science it has to be able to accept objective fact over subjective opinion, taxonomy has long been struggling to do that, and so cannot truly be called a science until it eliminates that completely. There is certainly room for subjectivity in science, but not when it overrides objective fact.

Right, so you think choosing subjective opinion over objective fact is scientific?

The taxonomy case is not unique in having subjective opinion generally be the more scientific route. A similar example is organic chemistry. Deoxyribonucleic acid versus the subjective, but far more widely adopted DNA. Adenosine triphosphate versus ATP. High density polyethylene versus HDPE.

On the other hand, you have crap like ringwoodite for a high pressure polymorph of olivine. Geology really doesn't fare well here.

The problem of taxonomy is that it is intended for people who want to use it to labe

The problem is that taxonomy isn't a science, it's a tool. It shows how different species are related morphologically and chemically and more recently genetically. It's a tool to used by other branches of biology to further their research, and now the tool has become too accurate for it's own good. Not really, but that's the perception. Part of the problem is that the dividing lines between species are artificial constructs, there's no line in the sand that says "everything on this side is a red bottle

I think the problem is that science is the study and subsequent authoring of knowledge based on observation and experiment. Historically, because we didn't know about DNA, you could in fact reasonably call taxonomy a science, because there was nothing unscientific about the fact that certain species seemed, given all evidence available, to be one species or another, one genus or another.

Then along came DNA analysis and it turns out some of that old science was wrong, the new science results in reclassificat

MyCleanPC and Golden Girls are passing fads, but this random-word-spam keeps coming year after year. The subject line usually has something like "mod d0wn" and the word "BSD" often appears in the body.

Interesting and mysterious. Somewhere there is hiding a machine and its operator who maintain this little tradition.

I don't care how many species are going extinct, there are enough unclassified species out there to keep taxonomists busy for the next 300 years.

The problem isn't decreasing diversity. It's the same problem with everything: we are getting too lazy to do the grunt work. Who wants to spend their time trying to decide where a creature fits into existing taxonomic trees when there's more "hollywood" type work to be done- you can get out on a Greenpeace boat and get sprayed with water cannons for trying to sav

"Computer" used to be a job description, not a piece of machinery. Businesses that had to do a lot of number crunching would hire rooms full of people who did nothing but arithmetic all day. Now we can do that easily with machines.

Sometimes, its a good thing that certain careers are going away. It means we can reserve our human brainpower for more important problems.